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3 Answers
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For the cubes, dump them out, in approximately the right spots; slide most of them over to the left, then make sure the 3 right-most cubes for each of tech/resources/money are in the right spots. Let people sort the rest when it's not their turn.

That said, I'd love to have boards that had recesses for all of the cubes/discs so they moved around less.

I've found through my plays of Eclipse that there are 4 things you can do to speed up setup:

1) Take the bags where you put the ships in for each player. Add 3 colony ships, the storage markers, the starbases, all cubes and disks. You'll have a bag for each player with all the stuff they need to setup their player board.

2) Buy a 'bead storage box'. Craft section of Michaels or Walmart. Put your sorted upgrades in here. Setting up the supply board is as simple as taking the lid off of this box and placing technology tiles.

3) Buy some Population Trays off the internet. These are specifically for eclipse. You can buy the ones with lids and that will let you store all the cubes for a given player in the tray. Setting up a player board is as simple as opening the lid and dumping the contents of their bag next to the board.

4) Have all other components pre-sorted and bagged seperately.

It takes < 5 minutes to go from putting the box on the table to making my first action with this setup.

Our group just uses the little plastic bags that come with the game and put everything for one player to start in one of them. We have the starting hex, the ships, the populations cubes, etc. all in the bag. We only set up the rightmost population cube. We can get started in as little as 5 minutes.